Maximizing the Efficiency of Genotyping-By-Sequencing

Introduction

Next-generation sequencing (NGS) platforms dramatically increase the rate of acquiring genomic and genotypic information, allowing faster and more accurate breeding decisions that make a difference on farms everywhere. In order for these platforms to be cost-efficient and a viable alternative to PCR-based genotyping, ideal operating efficiency must be realized.

Situation

A multinational seed company was utilizing a genotyping-by-sequencing (GBS) protocol on their NGS platform in support of several row crop breeding programs. The company had initially experienced a high number of no barcode reads using desalted adapters. In an effort to maximize marker data obtained per sequencing run, the company began using HPLC-purified adapters and barcodes. The higher purity adapters greatly decreased the number of no barcode reads, but the higher cost of HPLC purification increased overall costs. The company chose Sigma-Aldrich to help develop a solution to balance cost and sequencing efficiency.

Solution

With 25 years of experience manufacturing custom oligonucleotides, Sigma-Aldrich understood the importance of adapter purity in minimizing no barcode reads. Using in-house, proprietary technology, the company’s adapters and barcodes were synthesized and purified to provide HPLC-like results at 60% less cost.

Additionally, Sigma-Aldrich developed a manufacturing process to accommodate high-throughput demand and a validation plan to implement the new adapters on the company’s sequencing platform. As a result of the collaboration with Sigma-Aldrich, the company was able to decrease no barcode reads by >50%, maximize the efficiency of their NGS platform and lower overall cost per marker.

A Focus On Agriculture

At Sigma-Aldrich, our experience and dedicated agricultural resources, combined with our global reach, make us the ideal partner to help you achieve your goals. We have the tools, products and systems in place that allow you to create the solutions that growers everywhere need to help feed the world.

Explore How We Can Improve Your Workflow

Visit sigma-aldrich.com/agriculture

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